Extended Data Fig. 10: CREB1 deletion in DNMT-TKO neurons causes reduced chromatin accessibility and transcription.
a, Scheme of Creb1 with exons in black and CRISPR cut site indicated by green triangle. Sequence below displays a 5 bp deletion in CREB1-deleted DNMT-TKO neurons. b, Western blot detecting CREB1 in nuclear extracts from WT and DNMT-TKO ES cells, which is absent in CREB1-KO cells. Lamin serves as a loading control. Blot is representative of three independent experiments. c, Unsupervised clustering of RNA-seq signals from WT and mutant neuron cells (RPKM). PCC, Pearson’s correlation coefficient. d, Volcano plot showing gene expression changes between WT or CREB1-deleted DNMT-TKO neurons. Differentially expressed genes (FDR = < 0.01 and |log2FC| >= 1) indicated by dashed lines. Orange circled points are genes that are bound by CREB1 in their promoter region, as determined by ChIP-seq. Fsip2l is indicated by a blue dot. e, Unsupervised clustering of ATAC-seq samples in all CREB1 peak regions from WT, DNMT-TKO or CREB1-KO in DNMT-TKO neurons. Colors indicate pairwise Pearson’s correlation coefficients (PCC) of log-transformed normalized read counts in ATAC-seq peaks, indicating reproducibility between replicates and separation of all three genotypes. f, Changes in chromatin accessibility (ATAC-seq) binned by CREB1 enrichments in absence of DNA methylation. Accessibility changes between WT and DNMT-TKO neurons (left) and between WT and CREB1-deleted DNMT-TKO neurons (right). Replicate samples per condition (n = 3) are combined. Number of data points indicated. Boxplots as in Fig. 2d.
